I am currently writing a macro script to find the length of plant roots. In order to do so I am using the analyse skeleton plugin which allows me to find the longest shortest path. However, due to some noise in the background there are a lot of extra unwanted ROIs.
I have seen that you could also apply analyse partices on the skeleton image which outputs ROI based on size (pixel^2), but it does not give me the shortest longest path.
In my head, there are 3 different scenarios to solve this which I have not found the answer to:
- Is there a way to use the ROI manager data from the analyse particles and feed it into the analyse skeleton (2D/3D) plugin to find the shortest longest path of the selected ROIs?
- Is there just a simple plugin/ built in tool in Fiji that allows me to find the shortest longest path of the ROIs?
- Is there a way to just atomically filter in the analyse skeleton based on size (pixel^2) as in analyse particles?
Any help or suggestion is appreciated.